Extended Data Table 1. 230 ancient individuals analyzed in this study.
Population: samples grouped by a combination of date, source, archaeology and genetics. Date range: approximate date range of samples in this group. N: Number of individuals sampled. Out: Number of PCA outliers (marked with an asterisk if used in selection analysis). Rel: Number of related individuals removed. Eff N Chr: Average over sites of the effective number of chromosomes when we use genotype likelihoods. Computed as 2 per called site for samples with genotype calls, or 2 – 0.5(c−1) for samples with read depth c. Selection population 1: Coarse population labels (marked with a caret if not used in genome-wide scan) Selection population 2: Fine population labels. Abbreviations: [E/M/L]N Early/Middle/Late Neolithic, LBK Linearbandkeramik, [E/S/W]HG Eastern/Scandinavian/Western hunter-gatherer, [E]BA [Early] Bronze Age, IA Iron Age.
| By population | Population | Date range | N | Out | Rel | Eff N Chr | Selection population 1 | Selection population 2 |
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| WHG | 8.2–8.0 kya | 3 | 0 | 0 | 4.66 | HG | HG | |
| Motala_HG | 7.9–7.5 kya | 6 | 0 | 0 | 5.19 | HG | HG | |
| Anatolia_Neolithic | 8.4–8.3 kya | 24 | 1 | 1 | 22.49 | EF | AN | |
| Hungary_EN | 7.7–7.7 kya | 10 | 0 | 0 | 8.81 | EF | CEM | |
| LBK_EN | 7.5–7.1 kya | 15 | 0 | 0 | 11.15 | EF | CEM | |
| Central_MN | 5.9–5.8 kya | 6 | 0 | 0 | 3.66 | EF | CEM | |
| lberia_EN | 7.3–7.2 kya | 4 | 0 | 1 | 3.54 | EF | INC | |
| lberia_MN | 5.9–5.6 kya | 4 | 0 | 0 | 3.47 | EF | INC | |
| lberia_Chalcolithic | 4.8–4.2 kya | 12 | 0 | 2 | 5.93 | EF | INC | |
| Remedello | 5.5–5.1 kya | 3 | 0 | 0 | 0.93 | EF | – | |
| Iceman | 5.4–5.1 kya | 1 | 0 | 0 | 1.90 | EF | – | |
| Central_LNBA | 4.9–4.6 kya | 35 | 1 | 2 | 17.55 | SA | CLB | |
| Yamnaya_Samara | 5.4–4.9 kya | 9 | 0 | 0 | 6.55 | SA | STP | |
| Yamnaya_Kalmykia | 5.3–4.7 kya | 6 | 0 | 0 | 3.50 | SA | STP | |
| Afanasievo | 5.3–5.0 kya | 5 | 0 | 0 | 3.01 | SA | STP | |
| Poltavka | 4.9–4.7 kya | 4 | 1* | 0 | 4.28 | SA | STP | |
| Sintashta | 4.3–4.1 kya | 5 | 0 | 0 | 2.35 | SA | STP | |
| Potapovka | 4.2–4.1 kya | 3 | 0 | 0 | 0.66 | SA | STP | |
| Srubnaya | 3.9–3.6 kya | 12 | 1* | 1 | 7.68 | SA | STP | |
| Andronovo | 3.8–3.6 kya | 3 | 1* | 0 | 3.87 | SA | STP | |
| Russia_EBA | 4.9–4.5 kya | 1 | 0 | 0 | 0.21 | SA | – | |
| Northern_LNBA | 4.9–4.5 kya | 10 | 0 | 0 | 3.81 | SA | – | |
| Bell_Beaker_LN | 4.5–4.5 kya | 17 | 0 | 1 | 6.64 | SAˆ | CLB | |
| Hungary_BA | 4.2–4.1 kya | 12 | 0 | 0 | 4.18 | SAˆ | CLB | |
| EHG | 7.7–7.6 kya | 3 | 0 | 0 | 2.15 | – | – | |
| Samara_Eneolithic | 7.2–6.0 kya | 3 | 0 | 0 | 1.07 | – | – | |
| Scythian_IA | 2.4–2.2 kya | 1 | 0 | 0 | 1.26 | – | – | |
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| By selection population | Selection population 1 | Date range | N | Out | Rel | Eff N Chr | Description | |
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| EF | 8.4–4.2 kya | 79 | 0 | 0 | 61.88 | Early Farmer | ||
| HG | 8.2–7.5 kya | 9 | 0 | 0 | 9.85 | Hunter-gatherer | ||
| SA | 5.4–3.6 kya | 93 | 3 | 0 | 52.14 | Steppe Ancestry | ||
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| Selection population 2 | Date range | N | Out | Rel | Eff N Chr | Description | ||
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| AN | 8.4–8.3 kya | 24 | 0 | 0 | 22.49 | Anatolian Neolithic | ||
| CEM | 7.7–5.8 kya | 31 | 0 | 0 | 23.62 | Central European Early and Middle Neolithic | ||
| INC | 7.3–4.2 kya | 20 | 0 | 0 | 12.95 | Iberian Neolithic and Chalcolithic | ||
| HG | 8.2–7.5 kya | 9 | 0 | 0 | 9.85 | Hunter-gatherer | ||
| CLB | 4.9–4.1 kya | 64 | 0 | 0 | 28.38 | Central European Late Neolithic and Bronze Age | ||
| STP | 5.4–3.6 kya | 47 | 3 | 0 | 30.58 | Steppe | ||